[Biopython] comparing micro array data

[Vincent Davis]

>
> @ Sean

I would suggest finding a

local collaborator if you are relatively new to the microarray field.


I actually was brought into this project by a team from an university. They
know lots including that this is a difficult problem. They did not have any
references as to how others have solved this problem with whatever success
was possible. Since I know python, biopython has been my first choice to ask
other smart people :)


I am an economist. I am ok with the stats and data but don't know the
terminology well, It's been a 3 week crash course in my free time. I wrote
my own modules for reading in CEL and  CDF files as python objects. I know
there are existing solution but I would not learned as much that way. I used
the nexalign program that was recommended on this list to get the mismatch
data. It's all coming along nicely andI am learning lots. The prject has
been languishing for a list of reasons and now there is a push to get it
finished.

  *Vincent Davis
720-301-3003 *
vincent at vincentdavis.net
 my blog <http://vincentdavis.net> |
LinkedIn<http://www.linkedin.com/in/vincentdavis>


On Tue, Mar 16, 2010 at 10:38 AM, Sean Davis <sdavis2 at mail.nih.gov> wrote:

> On Tue, Mar 16, 2010 at 11:03 AM, Vincent Davis
> <vincent at vincentdavis.net> wrote:
> > So I am very new to this so please accept my ignorance on this subject.
> >
> > I have several micro array samples ~ 8 for each of 3 known genomes. So I
> > know which probes/sequences are a match and which have close matches. I
> > would like to identify which sequences exist in an unknown sample. The
> array
> > is custom and there is little to know overlap between probes.
> > What is the "standard" way of doing this? I don't care to know if a SNP
> is
> > present only if the sequence is present.
> > Is this standard available in biopython ?
>
> Hi, Vincent.  I'm not clear on what the study is here.  Could you
> explain a bit more what you are doing?  I get the suggestion from your
> email that you want to do a cross-species comparison using
> microarrays.  If this is the case, this is notoriously difficult to
> do, so, in addition to the comments here, I would suggest finding a
> local collaborator if you are relatively new to the microarray field.
>
> Sean
>